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Widespread Denisovan ancestry in Island Southeast Asia but no evidence of substantial super-archaic hominin admixture

Abstract

The hominin fossil record of Island Southeast Asia (ISEA) indicates that at least two endemic ‘super-archaic’ species—Homo luzonensis and H. floresiensis—were present around the time anatomically modern humans arrived in the region >50,000 years ago. Intriguingly, contemporary human populations across ISEA carry distinct genomic traces of ancient interbreeding events with Denisovans—a separate hominin lineage that currently lacks a fossil record in ISEA. To query this apparent disparity between fossil and genetic evidence, we performed a comprehensive search for super-archaic introgression in >400 modern human genomes, including >200 from ISEA. Our results corroborate widespread Denisovan ancestry in ISEA populations, but fail to detect any substantial super-archaic admixture signals compatible with the endemic fossil record of ISEA. We discuss the implications of our findings for the understanding of hominin history in ISEA, including future research directions that might help to unlock more details about the prehistory of the enigmatic Denisovans.

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Fig. 1: Introgression signals in extant populations across ISEA.
Fig. 2: Results from coalescent simulations exploring the detection of archaic hominin introgressed sequences.
Fig. 3: Hominin occupation and megafauna survival in ISEA at the time of modern human arrival.

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Data availability

The genetic datasets analysed during the current study were downloaded from, and are available at, the European Genome-phenome Archive (accession number EGAS00001003054; https://www.ebi.ac.uk/ega/home) and the Estonian Biocentre data archive (http://evolbio.ut.ee).

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Acknowledgements

We thank C. Huber and J. Schmidt for useful discussions on the genetic analyses, and K. Mitchell and F. Racimo for comments on the manuscript. This work was supported by ARC Indigenous Discovery Grant IN180100017 (J.C.T. and R.T.) and ARC Laureate Fellowships FL100100195 (C.S.M.T.) and FL140100260 (A.C.). C.S. acknowledges funding from the Calleva Foundation and The Human Origins Research Fund. G.S.J. acknowledges support from a Presidential Postdoctoral Fellowship from Nanyang Technological University.

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J.C.T., K.M.H., G.S.J., M.P.C., G.H., G.A.P. and J.T. designed the methods and undertook the analyses. J.C.T., K.M.H., R.T., G.S.J., H.S., A.C., C.S., C.S.M.T. and M.P.C. wrote the manuscript with input from all authors.

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Correspondence to João C. Teixeira.

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Peer review information Nature Ecology & Evolution thanks Laurits Skov and the other, anonymous, reviewer(s) for their contribution to the peer review of this work.

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Teixeira, J.C., Jacobs, G.S., Stringer, C. et al. Widespread Denisovan ancestry in Island Southeast Asia but no evidence of substantial super-archaic hominin admixture. Nat Ecol Evol 5, 616–624 (2021). https://doi.org/10.1038/s41559-021-01408-0

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